It would be easy to hate these characters, wouldn't it? You could look at Tally at the beginning, talking about how pretty people are, and say,"she's so shallow." You could look at Shay, who runs away to the Smoke without even understanding about the Special Circumstances people, and say, "she's so naive and self-centered." You could look at David, trusting Tally without even knowing her and say, "He's too trusting—and his hair is stupid" (we're guessing).
But the book never invites us to look down on (most of) these characters, especially Tally. For instance, check out Tally at the end of the book, when Tally is struggling with her confession to David:
But no matter what David said now, he would always remember what she had done, the lives she had cost with her secrets. This was the only way Tally could be certain that he had forgiven her. If he came to rescue her, she would know. (50.12)
We could try to sneer at that: oh, Tally, always thinking about herself and whether a guy likes her. But it's hard to laugh, because it's such a serious moment for Tally: she feels guilty, and the only way to make sure that she's forgiven is to do something to make up for what she's done. It's not so easy to laugh at someone sacrificing something in order to redeem herself, is it?
And that's why we say this book is sympathetic. It presents the characters' feelings openly and clearly. We may not identify with these characters and feel what they're feeling, but the book lets us sympathize.
But that doesn't mean that this book isn't funny. It's funny in a dark, ironic way, like how often Tally tries to do one thing, but ends up doing the opposite.
For instance, she grabs a mask when she's in New Pretty Town to hide her ugliness—but it's a pig mask. She tries to hide herself with the mask—but the mask makes her very obvious to the pretties in Garbo Mansions. She decides to stay in the Smoke and destroys Dr. Cable's tracker to symbolize her new love for the Smoke—but her destruction of the tracker calls in Special Circumstances. She doesn't want to be pretty at the end—but that's when she gives herself up to be made pretty.
We could go on and on, but we've run out of dashes to use to separate what Tally wants from what she gets. All of these are examples of ironic twists. They're all kind of funny in an "oh, I recognize that" sort of way, but they're also kind of sad. Every time she tries to make her life better, she just ends up making it worse.